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uniprot_search

Read-only

Retrieve protein data from UniProtKB with flexible query syntax. Apply filters for reviewed status and organism.

Instructions

Search UniProtKB. Examples: '(gene:TP53) AND (organism_id:9606)', 'kinase AND reviewed:true'. Set reviewed_only=true for Swiss-Prot only. Set organism to taxonomy ID or name.

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
queryYes
sizeNo
reviewed_onlyNo
organismNo
response_formatNomarkdown

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior3/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

Annotations already declare readOnlyHint and openWorldHint, so the description adds minimal behavioral context. It does mention filtering behavior (reviewed_only, organism) but does not disclose other traits like pagination or rate limits.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

Short and front-loaded with the core action. Examples are useful but could be more structured. Still, efficient for the agent.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness3/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given the output schema exists, the description partially addresses key parameters. However, for a search tool with 5 parameters, only 2 are explained, leaving gaps in context for the agent.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters2/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

With 0% schema description coverage, the description must compensate. It explains reviewed_only and organism but ignores size and response_format. Query parameter is only hinted through examples, lacking formal semantics.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose4/5

Does the description clearly state what the tool does and how it differs from similar tools?

Description clearly states 'Search UniProtKB' and provides example queries, indicating it is the main search for protein entries. However, it does not explicitly differentiate from sibling search tools like uniprot_search_citations, which search specific sub-databases.

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines3/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

Examples and parameter descriptions (e.g., reviewed_only, organism) imply usage contexts, but the description lacks explicit guidance on when to use this tool versus alternatives (e.g., when to use uniprot_get_entry instead).

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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